Index

[.mmkin. mkin 0.9.43

[.mmkin. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.43

FOCUS_2006_DFOP_ref_A_to_B. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.43

FOCUS_2006_FOMC_ref_A_to_F. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

FOCUS_2006_HS_ref_A_to_F. mkin 0.9.43

FOCUS_2006_HS_ref_A_to_F. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.43

FOCUS_2006_SFO_ref_A_to_F. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

FOCUS_2006_datasets. mkin 0.9.43

FOCUS_2006_datasets. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

FOMC.solution. mkin 0.9.43

FOMC.solution. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

HS.solution. mkin 0.9.43

HS.solution. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

IORE.solution. mkin 0.9.43

IORE.solution. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

SFO.solution. mkin 0.9.43

SFO.solution. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

SFORB.solution. mkin 0.9.43

SFORB.solution. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

endpoints. mkin 0.9.43

endpoints. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

geometric_mean. mkin 0.9.43

geometric_mean. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

ilr. mkin 0.9.43

ilr. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkin

The R package mkin provides calculation routines for the analysis of chemical degradation data, including multicompartment kinetics as diff --git a/inst/web/mccall81_245T.html b/inst/web/mccall81_245T.html index 00338040..6266c0b5 100644 --- a/inst/web/mccall81_245T.html +++ b/inst/web/mccall81_245T.html @@ -2,7 +2,7 @@ -mccall81_245T. mkin 0.9.43 +mccall81_245T. mkin 0.9.42 @@ -32,7 +32,7 @@

- mkin 0.9.43 + mkin 0.9.42

Index

mkin version: 0.9.43 +

mkin version: 0.9.42 R version: 3.2.4 -Date of fit: Thu Mar 24 08:26:26 2016 -Date of summary: Thu Mar 24 08:26:26 2016 +Date of fit: Thu Mar 24 08:28:59 2016 +Date of summary: Thu Mar 24 08:28:59 2016 Equations: d_T245 = - k_T245_sink * T245 - k_T245_phenol * T245 @@ -124,7 +124,7 @@ d_anisole = + k_phenol_anisole * phenol - k_anisole_sink * anisole Model predictions using solution type deSolve -Fitted with method Port using 246 model solutions performed in 1.451 s +Fitted with method Port using 246 model solutions performed in 1.454 s Weighting: none diff --git a/inst/web/mkin_long_to_wide.html b/inst/web/mkin_long_to_wide.html index e58ce305..de36532f 100644 --- a/inst/web/mkin_long_to_wide.html +++ b/inst/web/mkin_long_to_wide.html @@ -2,7 +2,7 @@ -mkin_long_to_wide. mkin 0.9.43 +mkin_long_to_wide. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkin_wide_to_long. mkin 0.9.43

mkin_wide_to_long. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkinds. mkin 0.9.43

mkinds. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkinerrmin. mkin 0.9.43

mkinerrmin. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkinfit. mkin 0.9.43

mkinfit. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkin version: 0.9.43 +

mkin version: 0.9.42 R version: 3.2.4 -Date of fit: Thu Mar 24 08:26:29 2016 -Date of summary: Thu Mar 24 08:26:29 2016 +Date of fit: Thu Mar 24 08:29:01 2016 +Date of summary: Thu Mar 24 08:29:01 2016 Equations: d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent Model predictions using solution type analytical -Fitted with method Port using 64 model solutions performed in 0.205 s +Fitted with method Port using 64 model solutions performed in 0.195 s Weighting: none @@ -409,7 +409,7 @@ print(system.time(fit <- mkinfit(SFO_SFO, FOCUS_2006_D, solution_type = "eigen", quiet = TRUE)))

user system elapsed - 1.200 1.252 0.926 + 1.276 1.196 0.935

coef(fit)

diff --git a/inst/web/mkinmod.html b/inst/web/mkinmod.html index 0a361956..b3a396b9 100644 --- a/inst/web/mkinmod.html +++ b/inst/web/mkinmod.html @@ -2,7 +2,7 @@ -mkinmod. mkin 0.9.43 +mkinmod. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkinparplot. mkin 0.9.43

mkinparplot. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkinplot. mkin 0.9.43

mkinplot. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkinpredict. mkin 0.9.43

mkinpredict. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

user system elapsed - 0.008 0.020 0.005 + 0.008 0.020 0.004

system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), @@ -315,7 +315,7 @@ 201 20 4.978707 27.46227

user system elapsed - 0.008 0.012 0.003 + 0.000 0.024 0.003

system.time( print(mkinpredict(SFO_SFO, c(k_parent_m1 = 0.05, k_parent_sink = 0.1, k_m1_sink = 0.01), @@ -326,7 +326,7 @@ 201 20 4.978707 27.46227

user system elapsed - 0.056 0.000 0.052 + 0.052 0.000 0.052

diff --git a/inst/web/mkinresplot.html b/inst/web/mkinresplot.html index b5f32633..5a2388dc 100644 --- a/inst/web/mkinresplot.html +++ b/inst/web/mkinresplot.html @@ -2,7 +2,7 @@ -mkinresplot. mkin 0.9.43 +mkinresplot. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mkinsub. mkin 0.9.43

mkinsub. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

mmkin. mkin 0.9.43

mmkin. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

plot.mkinfit. mkin 0.9.43

plot.mkinfit. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

plot.mmkin. mkin 0.9.43

plot.mmkin. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

print.mkinds. mkin 0.9.43

print.mkinds. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

print.mkinmod. mkin 0.9.43

print.mkinmod. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

schaefer07_complex_case. mkin 0.9.43

schaefer07_complex_case. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

summary.mkinfit. mkin 0.9.43

summary.mkinfit. mkin 0.9.42

- mkin 0.9.43 + mkin 0.9.42

Index

Examples

  summary(mkinfit(mkinmod(parent = list(type = "SFO")), FOCUS_2006_A, quiet = TRUE))
 
-mkin version:    0.9.43 
+mkin version:    0.9.42 
 R version:       3.2.4 
-Date of fit:     Thu Mar 24 08:26:38 2016 
-Date of summary: Thu Mar 24 08:26:38 2016 
+Date of fit:     Thu Mar 24 08:29:11 2016 
+Date of summary: Thu Mar 24 08:29:11 2016 
 
 Equations:
 d_parent = - k_parent_sink * parent
 
 Model predictions using solution type analytical 
 
-Fitted with method Port using 35 model solutions performed in 0.099 s
+Fitted with method Port using 35 model solutions performed in 0.096 s
 
 Weighting: none
 
diff --git a/inst/web/synthetic_data_for_UBA.html b/inst/web/synthetic_data_for_UBA.html
index 56a646c1..9fb9d23e 100644
--- a/inst/web/synthetic_data_for_UBA.html
+++ b/inst/web/synthetic_data_for_UBA.html
@@ -2,7 +2,7 @@
 
   
     
-synthetic_data_for_UBA_2014. mkin 0.9.43
+synthetic_data_for_UBA_2014. mkin 0.9.42
 
 
 
@@ -32,7 +32,7 @@
     
   
     
-      mkin 0.9.43
+      mkin 0.9.42
       
         
            Index
diff --git a/inst/web/transform_odeparms.html b/inst/web/transform_odeparms.html
index 5e16551f..f12ede67 100644
--- a/inst/web/transform_odeparms.html
+++ b/inst/web/transform_odeparms.html
@@ -2,7 +2,7 @@
 
   
     
-transform_odeparms. mkin 0.9.43
+transform_odeparms. mkin 0.9.42
 
 
   
     
-      mkin 0.9.43
+      mkin 0.9.42
       
         
            Index
@@ -133,10 +133,10 @@ backtransform_odeparms(transparms, mkinmod,  transform_rates = TRUE, t
 fit <- mkinfit(SFO_SFO, FOCUS_2006_D, quiet = TRUE)
 summary(fit, data=FALSE) # See transformed and backtransformed parameters
 
-mkin version:    0.9.43 
+mkin version:    0.9.42 
 R version:       3.2.4 
-Date of fit:     Thu Mar 24 08:26:40 2016 
-Date of summary: Thu Mar 24 08:26:40 2016 
+Date of fit:     Thu Mar 24 08:29:12 2016 
+Date of summary: Thu Mar 24 08:29:12 2016 
 
 Equations:
 d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -144,7 +144,7 @@ d_m1 = + k_parent_m1 * parent - k_m1_sink * m1
 
 Model predictions using solution type deSolve 
 
-Fitted with method Port using 153 model solutions performed in 0.662 s
+Fitted with method Port using 153 model solutions performed in 0.654 s
 
 Weighting: none
 
diff --git a/inst/web/vignettes/FOCUS_D.html b/inst/web/vignettes/FOCUS_D.html
index 1f3c6677..964c1ad8 100644
--- a/inst/web/vignettes/FOCUS_D.html
+++ b/inst/web/vignettes/FOCUS_D.html
@@ -10,7 +10,7 @@
 
 
 
-
+
 
 Example evaluation of FOCUS Example Dataset D
 
@@ -64,7 +64,7 @@ img {
 
 Example evaluation of FOCUS Example Dataset D
 Johannes Ranke
-2016-03-23
+2016-03-24
 
 
 
@@ -135,10 +135,10 @@ print(FOCUS_2006_D)

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:06 2015 
-## Date of summary: Mon Jul 20 14:51:06 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:54 2016 
+## Date of summary: Thu Mar 24 08:30:54 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -146,7 +146,7 @@ print(FOCUS_2006_D)
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.66 s
+## Fitted with method Port using 153 model solutions performed in 0.659 s
 ## 
 ## Weighting: none
 ## 
@@ -185,9 +185,9 @@ print(FOCUS_2006_D)

Example evaluation of FOCUS Laboratory Data L1 to L3

@@ -91,17 +91,17 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

Since mkin version 0.9-32 (July 2014), we can use shorthand notation like SFO for parent only degradation models. The following two lines fit the model and produce the summary report of the model fit. This covers the numerical analysis given in the FOCUS report.

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet=TRUE)
 summary(m.L1.SFO)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:06 2015 
-## Date of summary: Mon Jul 20 14:51:07 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:54 2016 
+## Date of summary: Thu Mar 24 08:30:54 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.091 s
 ## 
 ## Weighting: none
 ## 
@@ -131,9 +131,9 @@ summary(m.L1.SFO)
 ## Residual standard error: 2.948 on 16 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##               Estimate t value    Pr(>t)    Lower   Upper
 ## parent_0      92.47000   67.58 2.170e-21 89.57000 95.3700
 ## k_parent_sink  0.09561   24.65 1.867e-14  0.08773  0.1042
@@ -181,10 +181,10 @@ summary(m.L1.SFO)

## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge.
 ## Convergence code is 1

summary(m.L1.FOMC, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:07 2015 
-## Date of summary: Mon Jul 20 14:51:07 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:55 2016 
+## Date of summary: Thu Mar 24 08:30:55 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -196,7 +196,7 @@ summary(m.L1.SFO)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 0.43 s
+## Fitted with method Port using 188 model solutions performed in 0.527 s
 ## 
 ## Weighting: none
 ## 
@@ -230,9 +230,9 @@ summary(m.L1.SFO)

## Residual standard error: 3.045 on 15 degrees of freedom ## ## Backtransformed parameters: -## Confidence intervals for internally transformed parameters are asymmetric. -## t-test (unrealistically) based on the assumption of normal distribution -## for estimators of untransformed parameters. +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 9.247e+01 65.150 4.044e-20 8.944e+01 9.550e+01 ## alpha 5.044e+06 1.271 1.115e-01 5.510e-08 4.618e+20 @@ -261,17 +261,17 @@ FOCUS_2006_L2_mkin <- mkin_wide_to_long(FOCUS_2006_L2)

Again, the SFO model is fitted and a summary is obtained:

m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
 summary(m.L2.SFO)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:07 2015 
-## Date of summary: Mon Jul 20 14:51:07 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:55 2016 
+## Date of summary: Thu Mar 24 08:30:55 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.094 s
+## Fitted with method Port using 41 model solutions performed in 0.099 s
 ## 
 ## Weighting: none
 ## 
@@ -301,9 +301,9 @@ summary(m.L2.SFO)
 ## Residual standard error: 5.51 on 10 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##               Estimate t value    Pr(>t)   Lower   Upper
 ## parent_0       91.4700   24.03 1.773e-10 82.9800 99.9500
 ## k_parent_sink   0.6629    9.31 1.525e-06  0.5218  0.8421
@@ -349,17 +349,17 @@ plot(m.L2.FOMC)
 mkinresplot(m.L2.FOMC)

summary(m.L2.FOMC, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:08 2015 
-## Date of summary: Mon Jul 20 14:51:08 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:56 2016 
+## Date of summary: Thu Mar 24 08:30:56 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.18 s
+## Fitted with method Port using 81 model solutions performed in 0.2 s
 ## 
 ## Weighting: none
 ## 
@@ -393,9 +393,9 @@ mkinresplot(m.L2.FOMC)
 ## Residual standard error: 2.628 on 9 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##          Estimate t value    Pr(>t)   Lower  Upper
 ## parent_0   93.770  50.510 1.173e-12 89.5700 97.970
 ## alpha       1.374   5.355 2.296e-04  0.9009  2.097
@@ -421,10 +421,10 @@ plot(m.L2.DFOP)

plot(m.L2.DFOP)

summary(m.L2.DFOP, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:10 2015 
-## Date of summary: Mon Jul 20 14:51:10 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:58 2016 
+## Date of summary: Thu Mar 24 08:30:58 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -433,7 +433,7 @@ plot(m.L2.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.793 s
+## Fitted with method Port using 336 model solutions performed in 0.903 s
 ## 
 ## Weighting: none
 ## 
@@ -467,9 +467,9 @@ plot(m.L2.DFOP)

## Residual standard error: 1.732 on 8 degrees of freedom ## ## Backtransformed parameters: -## Confidence intervals for internally transformed parameters are asymmetric. -## t-test (unrealistically) based on the assumption of normal distribution -## for estimators of untransformed parameters. +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 93.9500 NA NA NA NA ## k1 22.6700 NA NA NA NA @@ -498,17 +498,17 @@ FOCUS_2006_L3_mkin <- mkin_wide_to_long(FOCUS_2006_L3) plot(m.L3.SFO)

summary(m.L3.SFO)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:10 2015 
-## Date of summary: Mon Jul 20 14:51:10 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:58 2016 
+## Date of summary: Thu Mar 24 08:30:58 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.103 s
+## Fitted with method Port using 43 model solutions performed in 0.104 s
 ## 
 ## Weighting: none
 ## 
@@ -538,9 +538,9 @@ plot(m.L3.SFO)
 ## Residual standard error: 12.91 on 6 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##               Estimate t value    Pr(>t)    Lower    Upper
 ## parent_0      74.87000   8.853 5.776e-05 54.18000 95.57000
 ## k_parent_sink  0.02527   3.067 1.102e-02  0.01138  0.05612
@@ -574,17 +574,17 @@ plot(m.L3.SFO)

plot(m.L3.FOMC)

summary(m.L3.FOMC, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:11 2015 
-## Date of summary: Mon Jul 20 14:51:11 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:59 2016 
+## Date of summary: Thu Mar 24 08:30:59 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.187 s
+## Fitted with method Port using 83 model solutions performed in 0.208 s
 ## 
 ## Weighting: none
 ## 
@@ -618,9 +618,9 @@ plot(m.L3.FOMC)
 ## Residual standard error: 4.572 on 5 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##          Estimate t value    Pr(>t)   Lower    Upper
 ## parent_0  96.9700  21.310 2.108e-06 85.2800 108.7000
 ## alpha      0.4224   5.867 1.020e-03  0.2725   0.6546
@@ -640,10 +640,10 @@ plot(m.L3.FOMC)

plot(m.L3.DFOP)

summary(m.L3.DFOP, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:11 2015 
-## Date of summary: Mon Jul 20 14:51:11 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:59 2016 
+## Date of summary: Thu Mar 24 08:30:59 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -652,7 +652,7 @@ plot(m.L3.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.322 s
+## Fitted with method Port using 137 model solutions performed in 0.351 s
 ## 
 ## Weighting: none
 ## 
@@ -690,9 +690,9 @@ plot(m.L3.DFOP)

## Residual standard error: 1.439 on 4 degrees of freedom ## ## Backtransformed parameters: -## Confidence intervals for internally transformed parameters are asymmetric. -## t-test (unrealistically) based on the assumption of normal distribution -## for estimators of untransformed parameters. +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 97.75000 67.970 1.404e-07 93.75000 101.70000 ## k1 0.51620 7.499 8.460e-04 0.35650 0.74750 @@ -722,17 +722,17 @@ FOCUS_2006_L4_mkin <- mkin_wide_to_long(FOCUS_2006_L4) plot(m.L4.SFO)

summary(m.L4.SFO, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:12 2015 
-## Date of summary: Mon Jul 20 14:51:12 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:31:00 2016 
+## Date of summary: Thu Mar 24 08:31:00 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.101 s
+## Fitted with method Port using 46 model solutions performed in 0.116 s
 ## 
 ## Weighting: none
 ## 
@@ -762,9 +762,9 @@ plot(m.L4.SFO)
 ## Residual standard error: 3.651 on 6 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##                Estimate t value    Pr(>t)     Lower     Upper
 ## parent_0      96.440000   49.49 2.283e-09 91.670000 1.012e+02
 ## k_parent_sink  0.006541   12.50 8.008e-06  0.005378 7.955e-03
@@ -787,17 +787,17 @@ plot(m.L4.SFO)

plot(m.L4.FOMC)

summary(m.L4.FOMC, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:12 2015 
-## Date of summary: Mon Jul 20 14:51:12 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:31:00 2016 
+## Date of summary: Thu Mar 24 08:31:00 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.146 s
+## Fitted with method Port using 66 model solutions performed in 0.164 s
 ## 
 ## Weighting: none
 ## 
@@ -831,9 +831,9 @@ plot(m.L4.FOMC)
 ## Residual standard error: 2.315 on 5 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##          Estimate t value    Pr(>t)   Lower   Upper
 ## parent_0  99.1400  59.020 1.322e-08 94.8200 103.500
 ## alpha      0.7042   2.685 2.178e-02  0.2703   1.835
diff --git a/inst/web/vignettes/FOCUS_Z.pdf b/inst/web/vignettes/FOCUS_Z.pdf
index 8103cba4..3b804e88 100644
Binary files a/inst/web/vignettes/FOCUS_Z.pdf and b/inst/web/vignettes/FOCUS_Z.pdf differ
diff --git a/inst/web/vignettes/compiled_models.html b/inst/web/vignettes/compiled_models.html
index 756a2753..50db7e9a 100644
--- a/inst/web/vignettes/compiled_models.html
+++ b/inst/web/vignettes/compiled_models.html
@@ -10,7 +10,7 @@
 
 
 
-
+
 
 Performance benefit by using compiled model definitions in mkin
 
@@ -65,7 +65,7 @@ img {
 
 Performance benefit by using compiled model definitions in mkin
 Johannes Ranke
-2016-03-23
+2016-03-24
 
 
 
@@ -89,8 +89,10 @@ SFO_SFO <- mkinmod(
 ## Successfully compiled differential equation model from auto-generated C code.
 We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the microbenchmark package.
 library("microbenchmark")
-library("ggplot2")
-mb.1 <- microbenchmark(
+library("ggplot2")
+## Need help? Try the ggplot2 mailing list:
+## http://groups.google.com/group/ggplot2.
+mb.1 <- microbenchmark(
   "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
                                     solution_type = "deSolve", 
                                     use_compiled = FALSE, quiet = TRUE),
@@ -98,27 +100,29 @@ mb.1 <- microbenchmark(
                                solution_type = "eigen", quiet = TRUE),
   "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
                                 solution_type = "deSolve", quiet = TRUE),
-  times = 3, control = list(warmup = 1))
-
-smb.1 <- summary(mb.1)
+  times = 3, control = list(warmup = 0))
+## Warning in microbenchmark(`deSolve, not compiled` = mkinfit(SFO_SFO,
+## FOCUS_2006_D, : Could not measure overhead. Your clock might lack
+## precision.
+smb.1 <- summary(mb.1)
 print(mb.1)
 ## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 9539.3064 9543.1547 9554.1987 9547.0031 9561.6448
-##       Eigenvalue based  927.5569  928.1716  943.8293  928.7864  951.9656
-##      deSolve, compiled  734.6125  737.3273  739.0161  740.0420  741.2179
+##  deSolve, not compiled 9280.0854 9299.6757 9323.2559 9319.2659 9344.8411
+##       Eigenvalue based  885.7475  891.8548  907.2823  897.9621  918.0498
+##      deSolve, compiled  713.2624  721.4990  728.2856  729.7357  735.7972
 ##        max neval cld
-##  9576.2865     3   c
-##   975.1447     3  b 
-##   742.3938     3 a
+##  9370.4163     3   c
+##   938.1374     3  b 
+##   741.8588     3 a

autoplot(mb.1)

We see that using the compiled model is by a factor of 12.9 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

We see that using the compiled model is by a factor of 12.8 faster than using the R version with the default ode solver, and it is even faster than the Eigenvalue based solution implemented in R which does not need iterative solution of the ODEs:

rownames(smb.1) <- smb.1$expr
 smb.1["median"]/smb.1["deSolve, compiled", "median"]

##                          median
-## deSolve, not compiled 12.900624
-## Eigenvalue based       1.255046
+## deSolve, not compiled 12.770742
+## Eigenvalue based       1.230531
 ## deSolve, compiled      1.000000

@@ -132,23 +136,26 @@ smb.1["median"]/smb.1["deSolve, compiled", "median" "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, use_compiled = FALSE, quiet = TRUE), "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE), - times = 3, control = list(warmup = 1)) -smb.2 <- summary(mb.2) + times = 3, control = list(warmup = 0)) +

## Warning in microbenchmark(`deSolve, not compiled` = mkinfit(FOMC_SFO,
+## FOCUS_2006_D, : Could not measure overhead. Your clock might lack
+## precision.

smb.2 <- summary(mb.2)
 print(mb.2)

## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 20.728228 20.867978 20.959811 21.007729 21.075602
-##      deSolve, compiled  1.343219  1.382365  1.399697  1.421511  1.427936
-##        max neval cld
-##  21.143476     3   b
-##   1.434362     3  a

+## deSolve, not compiled 20.543131 20.661195 20.720383 20.779259 20.809008 +## deSolve, compiled 1.314865 1.316439 1.328049 1.318014 1.334642 +## max neval cld +## 20.83876 3 b +## 1.35127 3 a

smb.2["median"]/smb.2["deSolve, compiled", "median"]

##   median
 ## 1     NA
 ## 2     NA

autoplot(mb.2)

Here we get a performance benefit of a factor of 14.8 using the version of the differential equation model compiled from C code using the inline package!

Here we get a performance benefit of a factor of 15.8 using the version of the differential equation model compiled from C code using the inline package!

This vignette was built with mkin 0.9.42 on

## R version 3.2.4 Revised (2016-03-16 r70336)
 ## Platform: x86_64-pc-linux-gnu (64-bit)
diff --git a/inst/web/vignettes/mkin.pdf b/inst/web/vignettes/mkin.pdf
index b07cdc72..4e3863d6 100644
Binary files a/inst/web/vignettes/mkin.pdf and b/inst/web/vignettes/mkin.pdf differ
diff --git a/vignettes/FOCUS_D.html b/vignettes/FOCUS_D.html
index 1f3c6677..964c1ad8 100644
--- a/vignettes/FOCUS_D.html
+++ b/vignettes/FOCUS_D.html
@@ -10,7 +10,7 @@
 
 
 
-
+
 
 Example evaluation of FOCUS Example Dataset D
 
@@ -64,7 +64,7 @@ img {
 
 Example evaluation of FOCUS Example Dataset D
 Johannes Ranke
-2016-03-23
+2016-03-24
 
 
 
@@ -135,10 +135,10 @@ print(FOCUS_2006_D)

A comprehensive report of the results is obtained using the summary method for mkinfit objects.

summary(fit)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:06 2015 
-## Date of summary: Mon Jul 20 14:51:06 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:54 2016 
+## Date of summary: Thu Mar 24 08:30:54 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent - k_parent_m1 * parent
@@ -146,7 +146,7 @@ print(FOCUS_2006_D)
 ## 
 ## Model predictions using solution type deSolve 
 ## 
-## Fitted with method Port using 153 model solutions performed in 0.66 s
+## Fitted with method Port using 153 model solutions performed in 0.659 s
 ## 
 ## Weighting: none
 ## 
@@ -185,9 +185,9 @@ print(FOCUS_2006_D)

## Residual standard error: 3.211 on 36 degrees of freedom ## ## Backtransformed parameters: -## Confidence intervals for internally transformed parameters are asymmetric. -## t-test (unrealistically) based on the assumption of normal distribution -## for estimators of untransformed parameters. +## Confidence intervals for internally transformed parameters are asymmetric. +## t-test (unrealistically) based on the assumption of normal distribution +## for estimators of untransformed parameters. ## Estimate t value Pr(>t) Lower Upper ## parent_0 99.600000 61.720 2.024e-38 96.330000 1.029e+02 ## k_parent_sink 0.047920 12.780 3.050e-15 0.040890 5.616e-02 diff --git a/vignettes/FOCUS_L.html b/vignettes/FOCUS_L.html index a7564f72..25551855 100644 --- a/vignettes/FOCUS_L.html +++ b/vignettes/FOCUS_L.html @@ -10,7 +10,7 @@ - + Example evaluation of FOCUS Laboratory Data L1 to L3 @@ -65,7 +65,7 @@ img {

@@ -91,17 +91,17 @@ FOCUS_2006_L1_mkin <- mkin_wide_to_long(FOCUS_2006_L1)

m.L1.SFO <- mkinfit("SFO", FOCUS_2006_L1_mkin, quiet=TRUE)
 summary(m.L1.SFO)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:06 2015 
-## Date of summary: Mon Jul 20 14:51:07 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:54 2016 
+## Date of summary: Thu Mar 24 08:30:54 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 37 model solutions performed in 0.087 s
+## Fitted with method Port using 37 model solutions performed in 0.091 s
 ## 
 ## Weighting: none
 ## 
@@ -131,9 +131,9 @@ summary(m.L1.SFO)
 ## Residual standard error: 2.948 on 16 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##               Estimate t value    Pr(>t)    Lower   Upper
 ## parent_0      92.47000   67.58 2.170e-21 89.57000 95.3700
 ## k_parent_sink  0.09561   24.65 1.867e-14  0.08773  0.1042
@@ -181,10 +181,10 @@ summary(m.L1.SFO)

## Warning in mkinfit("FOMC", FOCUS_2006_L1_mkin, quiet = TRUE): Optimisation by method Port did not converge.
 ## Convergence code is 1

summary(m.L1.FOMC, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:07 2015 
-## Date of summary: Mon Jul 20 14:51:07 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:55 2016 
+## Date of summary: Thu Mar 24 08:30:55 2016 
 ## 
 ## 
 ## Warning: Optimisation by method Port did not converge.
@@ -196,7 +196,7 @@ summary(m.L1.SFO)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 188 model solutions performed in 0.43 s
+## Fitted with method Port using 188 model solutions performed in 0.527 s
 ## 
 ## Weighting: none
 ## 
@@ -230,9 +230,9 @@ summary(m.L1.SFO)

Again, the SFO model is fitted and a summary is obtained:

m.L2.SFO <- mkinfit("SFO", FOCUS_2006_L2_mkin, quiet=TRUE)
 summary(m.L2.SFO)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:07 2015 
-## Date of summary: Mon Jul 20 14:51:07 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:55 2016 
+## Date of summary: Thu Mar 24 08:30:55 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 41 model solutions performed in 0.094 s
+## Fitted with method Port using 41 model solutions performed in 0.099 s
 ## 
 ## Weighting: none
 ## 
@@ -301,9 +301,9 @@ summary(m.L2.SFO)
 ## Residual standard error: 5.51 on 10 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##               Estimate t value    Pr(>t)   Lower   Upper
 ## parent_0       91.4700   24.03 1.773e-10 82.9800 99.9500
 ## k_parent_sink   0.6629    9.31 1.525e-06  0.5218  0.8421
@@ -349,17 +349,17 @@ plot(m.L2.FOMC)
 mkinresplot(m.L2.FOMC)

summary(m.L2.FOMC, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:08 2015 
-## Date of summary: Mon Jul 20 14:51:08 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:56 2016 
+## Date of summary: Thu Mar 24 08:30:56 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 81 model solutions performed in 0.18 s
+## Fitted with method Port using 81 model solutions performed in 0.2 s
 ## 
 ## Weighting: none
 ## 
@@ -393,9 +393,9 @@ mkinresplot(m.L2.FOMC)
 ## Residual standard error: 2.628 on 9 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##          Estimate t value    Pr(>t)   Lower  Upper
 ## parent_0   93.770  50.510 1.173e-12 89.5700 97.970
 ## alpha       1.374   5.355 2.296e-04  0.9009  2.097
@@ -421,10 +421,10 @@ plot(m.L2.DFOP)

plot(m.L2.DFOP)

summary(m.L2.DFOP, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:10 2015 
-## Date of summary: Mon Jul 20 14:51:10 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:58 2016 
+## Date of summary: Thu Mar 24 08:30:58 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -433,7 +433,7 @@ plot(m.L2.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 336 model solutions performed in 0.793 s
+## Fitted with method Port using 336 model solutions performed in 0.903 s
 ## 
 ## Weighting: none
 ## 
@@ -467,9 +467,9 @@ plot(m.L2.DFOP)

summary(m.L3.SFO)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:10 2015 
-## Date of summary: Mon Jul 20 14:51:10 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:58 2016 
+## Date of summary: Thu Mar 24 08:30:58 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 43 model solutions performed in 0.103 s
+## Fitted with method Port using 43 model solutions performed in 0.104 s
 ## 
 ## Weighting: none
 ## 
@@ -538,9 +538,9 @@ plot(m.L3.SFO)
 ## Residual standard error: 12.91 on 6 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##               Estimate t value    Pr(>t)    Lower    Upper
 ## parent_0      74.87000   8.853 5.776e-05 54.18000 95.57000
 ## k_parent_sink  0.02527   3.067 1.102e-02  0.01138  0.05612
@@ -574,17 +574,17 @@ plot(m.L3.SFO)

plot(m.L3.FOMC)

summary(m.L3.FOMC, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:11 2015 
-## Date of summary: Mon Jul 20 14:51:11 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:59 2016 
+## Date of summary: Thu Mar 24 08:30:59 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 83 model solutions performed in 0.187 s
+## Fitted with method Port using 83 model solutions performed in 0.208 s
 ## 
 ## Weighting: none
 ## 
@@ -618,9 +618,9 @@ plot(m.L3.FOMC)
 ## Residual standard error: 4.572 on 5 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##          Estimate t value    Pr(>t)   Lower    Upper
 ## parent_0  96.9700  21.310 2.108e-06 85.2800 108.7000
 ## alpha      0.4224   5.867 1.020e-03  0.2725   0.6546
@@ -640,10 +640,10 @@ plot(m.L3.FOMC)

plot(m.L3.DFOP)

summary(m.L3.DFOP, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:11 2015 
-## Date of summary: Mon Jul 20 14:51:11 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:30:59 2016 
+## Date of summary: Thu Mar 24 08:30:59 2016 
 ## 
 ## Equations:
 ## d_parent = - ((k1 * g * exp(-k1 * time) + k2 * (1 - g) * exp(-k2 *
@@ -652,7 +652,7 @@ plot(m.L3.DFOP)
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 137 model solutions performed in 0.322 s
+## Fitted with method Port using 137 model solutions performed in 0.351 s
 ## 
 ## Weighting: none
 ## 
@@ -690,9 +690,9 @@ plot(m.L3.DFOP)

summary(m.L4.SFO, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:12 2015 
-## Date of summary: Mon Jul 20 14:51:12 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:31:00 2016 
+## Date of summary: Thu Mar 24 08:31:00 2016 
 ## 
 ## Equations:
 ## d_parent = - k_parent_sink * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 46 model solutions performed in 0.101 s
+## Fitted with method Port using 46 model solutions performed in 0.116 s
 ## 
 ## Weighting: none
 ## 
@@ -762,9 +762,9 @@ plot(m.L4.SFO)
 ## Residual standard error: 3.651 on 6 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##                Estimate t value    Pr(>t)     Lower     Upper
 ## parent_0      96.440000   49.49 2.283e-09 91.670000 1.012e+02
 ## k_parent_sink  0.006541   12.50 8.008e-06  0.005378 7.955e-03
@@ -787,17 +787,17 @@ plot(m.L4.SFO)

plot(m.L4.FOMC)

summary(m.L4.FOMC, data = FALSE)

## mkin version:    0.9.40 
-## R version:       3.2.1 
-## Date of fit:     Mon Jul 20 14:51:12 2015 
-## Date of summary: Mon Jul 20 14:51:12 2015 
+## mkin version:    0.9.42 
+## R version:       3.2.4 
+## Date of fit:     Thu Mar 24 08:31:00 2016 
+## Date of summary: Thu Mar 24 08:31:00 2016 
 ## 
 ## Equations:
 ## d_parent = - (alpha/beta) * 1/((time/beta) + 1) * parent
 ## 
 ## Model predictions using solution type analytical 
 ## 
-## Fitted with method Port using 66 model solutions performed in 0.146 s
+## Fitted with method Port using 66 model solutions performed in 0.164 s
 ## 
 ## Weighting: none
 ## 
@@ -831,9 +831,9 @@ plot(m.L4.FOMC)
 ## Residual standard error: 2.315 on 5 degrees of freedom
 ## 
 ## Backtransformed parameters:
-##   Confidence intervals for internally transformed parameters are asymmetric.
-##   t-test (unrealistically) based on the assumption of normal distribution
-##   for estimators of untransformed parameters.
+## Confidence intervals for internally transformed parameters are asymmetric.
+## t-test (unrealistically) based on the assumption of normal distribution
+## for estimators of untransformed parameters.
 ##          Estimate t value    Pr(>t)   Lower   Upper
 ## parent_0  99.1400  59.020 1.322e-08 94.8200 103.500
 ## alpha      0.7042   2.685 2.178e-02  0.2703   1.835
diff --git a/vignettes/FOCUS_Z.pdf b/vignettes/FOCUS_Z.pdf
index 8103cba4..3b804e88 100644
Binary files a/vignettes/FOCUS_Z.pdf and b/vignettes/FOCUS_Z.pdf differ
diff --git a/vignettes/compiled_models.html b/vignettes/compiled_models.html
index 3215a386..50db7e9a 100644
--- a/vignettes/compiled_models.html
+++ b/vignettes/compiled_models.html
@@ -1,248 +1,98 @@
 
-
-
-
-
-Benchmark for a model that can also be solved with Eigenvalues
 
-
+
 
-
-
+
+
+
-
-
 
-
-
-
-
+
 
 
+
+Performance benefit by using compiled model definitions in mkin
+Johannes Ranke
+2016-03-24
+
 
-
+
+
+Benchmark for a model that can also be solved with Eigenvalues
+Benchmark for a model that can not be solved with Eigenvalues
+
+
 
-
+
 Benchmark for a model that can also be solved with Eigenvalues
-
-This evaluation is taken from the example section of mkinfit. When using an mkin version
-equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see
-a message that the model is being compiled from autogenerated C code when
-defining a model using mkinmod. The mkinmod() function checks for presence of
-the gcc compiler using 
-
-Sys.which("gcc")
-
-
+This evaluation is taken from the example section of mkinfit. When using an mkin version equal to or greater than 0.9-36 and a C compiler (gcc) is available, you will see a message that the model is being compiled from autogenerated C code when defining a model using mkinmod. The mkinmod() function checks for presence of the gcc compiler using
+Sys.which("gcc")
 ##            gcc 
-## "/usr/bin/gcc"
-
-
+## "/usr/bin/gcc"

First, we build a simple degradation model for a parent compound with one metabolite.

- -

library("mkin")
-

- -

## Loading required package: minpack.lm
-## Loading required package: rootSolve
-## Loading required package: inline
-## Loading required package: methods
-## Loading required package: parallel
-

- -

SFO_SFO <- mkinmod(
+library("mkin")
+SFO_SFO <- mkinmod(
   parent = mkinsub("SFO", "m1"),
-  m1 = mkinsub("SFO"))
-
-
-## Successfully compiled differential equation model from auto-generated C code.
-
-
-We can compare the performance of the Eigenvalue based solution against the
-compiled version and the R implementation of the differential equations using
-the microbenchmark package.
-
-library("microbenchmark")
-library("ggplot2")
-mb.1 <- microbenchmark(
+  m1 = mkinsub("SFO"))
+## Successfully compiled differential equation model from auto-generated C code.
+We can compare the performance of the Eigenvalue based solution against the compiled version and the R implementation of the differential equations using the microbenchmark package.
+library("microbenchmark")
+library("ggplot2")
+## Need help? Try the ggplot2 mailing list:
+## http://groups.google.com/group/ggplot2.
+mb.1 <- microbenchmark(
   "deSolve, not compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
                                     solution_type = "deSolve", 
                                     use_compiled = FALSE, quiet = TRUE),
@@ -250,115 +100,81 @@ mb.1 <- microbenchmark(
                                solution_type = "eigen", quiet = TRUE),
   "deSolve, compiled" = mkinfit(SFO_SFO, FOCUS_2006_D, 
                                 solution_type = "deSolve", quiet = TRUE),
-  times = 3, control = list(warmup = 0))
-
-
+  times = 3, control = list(warmup = 0))

## Warning in microbenchmark(`deSolve, not compiled` = mkinfit(SFO_SFO,
 ## FOCUS_2006_D, : Could not measure overhead. Your clock might lack
-## precision.
-

- -

smb.1 <- summary(mb.1)
-print(mb.1)
-

- +## precision. +

smb.1 <- summary(mb.1)
+print(mb.1)

## Unit: milliseconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 4652.4576 4653.2263 4673.1220 4653.9950 4683.4543
-##       Eigenvalue based  749.7771  750.1327  764.7881  750.4882  772.2936
-##      deSolve, compiled  641.9152  647.6028  651.6533  653.2904  656.5223
+##  deSolve, not compiled 9280.0854 9299.6757 9323.2559 9319.2659 9344.8411
+##       Eigenvalue based  885.7475  891.8548  907.2823  897.9621  918.0498
+##      deSolve, compiled  713.2624  721.4990  728.2856  729.7357  735.7972
 ##        max neval cld
-##  4712.9136     3   c
-##   794.0990     3  b 
-##   659.7542     3 a
-

- -

autoplot(mb.1)
-

- -

We see that using the compiled model is by a factor of -7.1 -faster than using the R version with the default ode solver, and it is even -faster than the Eigenvalue based solution implemented in R which does not need -iterative solution of the ODEs:

- -

rownames(smb.1) <- smb.1$expr
-smb.1["median"]/smb.1["deSolve, compiled", "median"]
-

- -

##                         median
-## deSolve, not compiled 7.123930
-## Eigenvalue based      1.148782
-## deSolve, compiled     1.000000
-

- +## 9370.4163 3 c +## 938.1374 3 b +## 741.8588 3 a +

autoplot(mb.1)

rownames(smb.1) <- smb.1$expr
+smb.1["median"]/smb.1["deSolve, compiled", "median"]

##                          median
+## deSolve, not compiled 12.770742
+## Eigenvalue based       1.230531
+## deSolve, compiled      1.000000

Benchmark for a model that can not be solved with Eigenvalues

- -

This evaluation is also taken from the example section of mkinfit.

- -

FOMC_SFO <- mkinmod(
+This evaluation is also taken from the example section of mkinfit.
+FOMC_SFO <- mkinmod(
   parent = mkinsub("FOMC", "m1"),
-  m1 = mkinsub( "SFO"))
-
-
-## Successfully compiled differential equation model from auto-generated C code.
-
-
-mb.2 <- microbenchmark(
+  m1 = mkinsub( "SFO"))
+## Successfully compiled differential equation model from auto-generated C code.
+mb.2 <- microbenchmark(
   "deSolve, not compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, 
                                     use_compiled = FALSE, quiet = TRUE),
   "deSolve, compiled" = mkinfit(FOMC_SFO, FOCUS_2006_D, quiet = TRUE),
-  times = 3, control = list(warmup = 0))
-
-
+  times = 3, control = list(warmup = 0))

## Warning in microbenchmark(`deSolve, not compiled` = mkinfit(FOMC_SFO,
 ## FOCUS_2006_D, : Could not measure overhead. Your clock might lack
-## precision.
-

- -

smb.2 <- summary(mb.2)
-print(mb.2)
-

- +## precision. +

smb.2 <- summary(mb.2)
+print(mb.2)

## Unit: seconds
 ##                   expr       min        lq      mean    median        uq
-##  deSolve, not compiled 10.202245 10.243829 10.260112 10.285413 10.289045
-##      deSolve, compiled  1.176863  1.182699  1.188555  1.188536  1.194402
-##        max neval cld
-##  10.292677     3   b
-##   1.200267     3  a
-

- -

smb.2["median"]/smb.2["deSolve, compiled", "median"]
-

- +## deSolve, not compiled 20.543131 20.661195 20.720383 20.779259 20.809008 +## deSolve, compiled 1.314865 1.316439 1.328049 1.318014 1.334642 +## max neval cld +## 20.83876 3 b +## 1.35127 3 a +

smb.2["median"]/smb.2["deSolve, compiled", "median"]

##   median
 ## 1     NA
-## 2     NA
-

+## 2 NA +

autoplot(mb.2)

Here we get a performance benefit of a factor of 15.8 using the version of the differential equation model compiled from C code using the inline package!

This vignette was built with mkin 0.9.42 on

## R version 3.2.4 Revised (2016-03-16 r70336)
+## Platform: x86_64-pc-linux-gnu (64-bit)
+## Running under: Debian GNU/Linux 8 (jessie)

## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz

autoplot(mb.2)
-

Here we get a performance benefit of a factor of -8.7 -using the version of the differential equation model compiled from C code using -the inline package!

## CPU model: Intel(R) Core(TM) i7-4710MQ CPU @ 2.50GHz
-